April 27, 2011

Single Out-of-Africa origin of humans: more trouble for the theory

The single recent Out-of-Africa (SROOA) model has been the "default position" in the scientific community for a long time, and it has found its way to popular consciousness by a number of TV documentaries and magazine articles.

This model has recently been shaken by the discovery that some modern humans are closer to extinct hominins: the Neandertals and Denisovans. Within SROOA this is quite unexpected, as these groups were thought to be irrelevant side branches of the human family tree: differential affiliation of some modern humans to them means that they are not.

This has invariably led to an acceptance that SROOA is basically wrong in its purist form, and an alternative form including some assimilation of archaic hominins is moving to become the new default position.

Now, a new paper that works within the SROOA tradition itself finds another surprising piece of evidence that contradicts SROOA. But, first, let's examine what SROOA entails:

A human group (Proto-Eurasians) moved Out of Africa, starting to become differentiated from Africans

At a later time, different Proto-Eurasian groups became effectively separated by geography and started diverging from each other, eventually evolving to become Europeans, East Asians, Australian Aborigines, etc.

Under this model, different Eurasian groups are expected to have exactly the same position vis a vis Africans, once drift is accounted for. Each population's divergence from Africans can be analyzed into two components, e.g., an African-Proto-Eurasian one, and a Proto-Eurasian-Chinese one. The genetic drift (away from Africans) in the first part is the same for all non-African populations (e.g., Chinese or Tuscans), while in the latter it is dependent on population history.

The new paper shows why this model is wrong: Europeans are closer to Africans than East Asians are. This is totally unexpected under SROOA, as Europeans are expected to be as distant from Africans as any other Eurasian group (once drift is accounted for).

I had noticed this phenomenon in my experiments for quite some time, and highlighted the possibility that haplogroup E1b1b, which is shared by West Eurasians and Africans may have something to do with it.

If autosomally African-like populations moved out of Africa carrying these Y-chromosomes, then we would expect only E1b1b-bearing populations to be shifted towards Africans relative to the Chinese. The authors rightly reject this idea because they discover that all European populations, including a wide variety of North European ones, where haplogroup E is non-existent, are closer to Africans than the Chinese are.

So, we are left with a bit of a problem:

There is clearly something "common" between West Eurasians (even North Europeans) and Sub-Saharan Africans that is not shared by East Asians, a factor X which brings them closer to each other than would be expected by the SROOA

The best candidate of this "common" element (Y-haplogroup E) does not have the expected distribution.

The problem can be solved in either of two ways. I have argued for both of them at some time or another, so it would be a good idea for a paper to come out and consider how one could be preferred over the other.

Solution #1: West Eurasian Back-Migration into Africa

The first solution is based on the idea that there has been a major episode of back-migration into Africa that is not captured by the standard model. Clearly, this cannot have been a recent event, as Sub-Saharan Africans largely lack (except in the North and East) certifiably West Eurasian derived markers. But, the event need not have been particularly recent: as long as it occurred after West Eurasians began to diverge from East Asians it would have established the genetic closeness observed by the authors.

I believe that the best signal of such a potential back-migration involves haplogroup E. This is the dominant patrilineage of black Africans by far, and almost certainly had an African (and probably an east African) origin. However, its sister haplogroup D occurs as a relic in Asia, among people such as Tibetans, Ainu, or Andaman Islanders. Where did the ancestral clade DE develop? If I was a betting man, I would say that somewhere between the Indian Ocean (where the Andamanese live), and East Africa.

An early movement of DE-bearing men from Arabia into East Africa would serve to bring a West Eurasian autosomal component into Africa. That component would then evolve into E in East Africa itself, and go on to (almost) completely replace pre-existing African Y-chromosomes, leaving haplogroups A and B at high frequencies in a few relic African hunter-gatherer populations.

From the Eurasian perspective, the problem would evaporate: West Eurasians' autosomal shift to Africans is not correlated with haplogroup E frequencies, because the latter was not initially associated with a Sub-Saharan-like autosomal gene pool.

Solution #2: Archaic admixture in East Asians

A second potential solution would interpret African-West Eurasian closeness not as evidence of a common population element in West Eurasians and Africans, but as a consequence of a population element in East Asians that both West Eurasians and Africans lack.

The obvious candidate for such an element involves archaic admixture in East Asians. This is no longer an exotic possibility, given the evidence for such admixture that the sequencing of the Neandertal and Denisovan genome has produced.

Under this scenario, Europeans and East Asians are genetically close because of their common Proto-Eurasian ancestry, and they both shared an initial same distance to Africans, but East Asians diverged from both West Eurasian and African populations by admixing with archaic humans they encountered in the East.

A test of solution #1

Suppose that solution #1 is correct. Consider also that:

West Eurasians are shifted relative to East Eurasians by x% to San Bushmen (who have some of the highest frequencies of non-E chromosomes), and are expected to be least affected by any sort of West Eurasian->Africa back-migration. C

West Eurasians are shifted relative to East Eurasians by y% to Yoruba (who have extremely high E-haplogroup frequencies), and are expected to be more affected by West-Eurasian->Africa back-migration than the San are.

If y is larger than x, then the prediction of the theory is supported.

It is not clear to me whether East Asian archaics/West Eurasian back-migration into Africa, or a combination of these factors may account for the observed phenomenon. I should point out a second Out-of-Africa expansion into West Eurasia (the authors' preferred model) is also not out of the question, but this cannot be easily tied to a particular event in prehistory or uniparental marker.

The study of human origins has just gotten even more interesting...

Genome Research doi:10.1101/gr.119636.110

Human population dispersal “Out of Africa” estimated from linkage disequilibrium and allele frequencies of SNPs

Brian P. McEvoy et al.

Abstract

Genetic and fossil evidence supports a single, recent (less than 200,000 yr) origin of modern Homo sapiens in Africa, followed by later population divergence and dispersal across the globe (the “Out of Africa” model). However, there is less agreement on the exact nature of this migration event and dispersal of populations relative to one another. We use the empirically observed genetic correlation structure (or linkage disequilibrium) between 242,000 genome-wide single nucleotide polymorphisms (SNPs) in 17 global populations to reconstruct two key parameters of human evolution: effective population size (Ne) and population divergence times (T). A linkage disequilibrium (LD)–based approach allows changes in human population size to be traced over time and reveals a substantial reduction in Ne accompanying the “Out of Africa” exodus as well as the dramatic re-expansion of non-Africans as they spread across the globe. Secondly, two parallel estimates of population divergence times provide clear evidence of population dispersal patterns “Out of Africa” and subsequent dispersal of proto-European and proto-East Asian populations. Estimates of divergence times between European–African and East Asian–African populations are inconsistent with its simplest manifestation: a single dispersal from the continent followed by a split into Western and Eastern Eurasian branches. Rather, population divergence times are consistent with substantial ancient gene flow to the proto-European population after its divergence with proto-East Asians, suggesting distinct, early dispersals of modern H. sapiens from Africa. We use simulated genetic polymorphism data to demonstrate the validity of our conclusions against alternative population demographic scenarios.

26 comments:

Maybe a hypothetical solution#3 could be gene flow through the strait of Gibraltar already in the Paleolithic. One of the assumptions of the OOA model is the idea that no human populations crossed the sea at that point in prehistory, but we know these crossings actually happened in other places. Maybe a limited population flow from N. Africa would explain some of the genetic components of European populations. Later on, post-glacial expansion from Iberia would explain the rest.

I haven't read the article yet, but on the basis of your summary and their abstract, I see two problems:

1. I don't think it meaningful to compare "proto-Europeans" with "proto-East Asians" because such a highly generalized comparison leaves out all the many indigenous groups scattered througout so much of Asia, particularly the Southeast, and also Melanesia and Australia. These regions are home to many populations that are very different in a great many ways from the rest of Asia.

2. I don't think you can generalize on such a large scale without taking into account the significant gap we find between African and East Asia, both culturally and genetically. The gap is centered in South Asia, which isn't even taken into account by the authors, apparently.

As indicated in my book, the most likely suspect is the much debated Toba event, but other events of comparable significance could also account for it.

History is full of contingencies and the possibility of such contingencies must always be taken into account, which is why results gleaned from mathematical modeling must always be taken with a grain of salt.

Well, which is it? Is x greater than y or vice versa? From the looks of the Nei and Φst tables, West Africans are further from Europeans than are the seemingly older San. Thus, the amount of hybridizing with the parent chronospecies must have been sufficient to outweigh all the E1b1b in-migration.

The Mbuti are furthest of all, yet their uniparental markers are more recent than those of the San. Either the San are admixed with East Africans or the Pygmies mixed with archaics the most.

A non-African origin of hg E has to explain why there is not more hg E diversity outside of Africa, and why European hg E types are a subset of African hg E types that has phylogenetic roots connecting them that are found only in Africa.

It also has to explain trace presence of very basal versions of Y-DNA hg D in West Africa, apparently unrelated to any recent migrations from e.g. Tibet where basal hgs of Y-DNA hg D are found, while there is an absence of even trace levels of Y-DNA hg E in Asian locations that are rich in Y-DNA hg D (e.g. Andaman Islands, Siberia, Tibet, Japan).

* * *

Moreover, one doesn't need a non-African origin for Y-DNA hg E to get the same genetic profile as the one you suggest from your Scenario One.

All you need is for back migration from SW Asia to East Africa (at some point after West Eurasians and East Eurasians become distinct) to produce introgression of SW Asian genes in an African population that contains the Y-DNA hg E population in East Africa that subsequently expands (presumably driven by the African Sahel Neolithic, or the arrival of domesticated herd animals, or some other technological advance) to become predominant in Africa.

Given the geographic proximity of East African and West Eurasia, and the fact that there are known back migrations into Africa (e.g. mtDNA hg M1), this is a highly plausible scenario.

* * *

One can also devise a scenario of low level subsequent migration out of Africa that makes sense to explain the autosomal similarities of Africans being closer than Asians.

We know that there was some relatively modern (probably Neolithic or later) migration of people from sub-Saharan Africa into SW Asia, Southern Europe, and North Africa, and that the percentage of admixture were on the order of low single digit percentages. If this admixture reached fixation in the population, you would get a population with a near universal low single digit percentage autosomal African component, a very low single digit African Y-DNA component, and a very low single digit African mtDNA component.

If Northern Europe is then settled by fairly small founder populations from the regions where African Y-DNA and mtDNA hgs are present, and that founder population lacks, due to random chance, the low frequency African Y-DNA and mtDNA hgs, then Northern Europeans are going to have low frequency African autosomal DNA, but no African Y-DNA or mtDNA hgs.

Nice summary. This is not unexpected, classical markers had shown the greater similarity of Europeans and Africans more than 20 years ago, but it was not trivial to exclude ascertainment as an explanation.

I am receptive to the idea of more admixture yet to be found in East Asia -- especially notice the Garrigan and Hammer arguments in favor of this -- but we have some indicators that might show whether this is very extensive (say more than 1-2%) that do not point to it.

I've noticed the greater similarity consistentlyin my own ADMIXTURE experiments in terms of Fst divergence (which can be influenced by ascertainment bias or drift).

What I find puzzling, however, are the results of the Reich et al. "Denisovan" paper wherein Table S6.2 shows genetic divergence times of Han/French vs. San/Yoruba that are quite nearly the same.

A non-African origin of hg E has to explain why there is not more hg E diversity outside of Africa, and why European hg E types are a subset of African hg E types that has phylogenetic roots connecting them that are found only in Africa.

I did not claim a Non-African origin of E, only a Non-African origin of the ancestor of E.

I have a fourth theory/ idea: East Eurasians evolved further from Africans because a smaller population in East Eurasia allowed new mutations to spread faster through the population or because the different environment drove East Eurasian evolution differently.

I don't think that African admixture in Eurasia through demic diffusion should be dismissed so easily because of the lack of Y-DNA E in parts of West Eurasia.

Of course, another possibility is a combination of ancient West Eurasian admixture in Africa and ancient African admixture in West Eurasia, or other events like a second OOA migration. Today, DE* is more common in West Africa than it is in Asia.

Another thing to keep in mind is that East Asians, who have some DE, are closer to Africans than the native inhabitants of the Americas, who largely lack DE.

"The new paper shows why this model is wrong: Europeans are closer to Africans than East Asians are. This is totally unexpected under SROOA, as Europeans are expected to be as distant from Africans as any other Eurasian group (once drift is accounted for)".

This is not true: Europeans (better: West Eurasians in general) have been receiving genetics from Africa (and giving them back) through at least specific Paleolithic episodes. This is most obvious in the penetration of Y-DNA haplogroup E (specifically E1b1b1), of clear recent African origin in almost all Europe. Maybe it's just a few percent in average (5%??) and clinal (i.e. filtered by North Africa and Arabia Peninsula) but enough to make a difference: East Asians had nothing of that.

"However, these Y chromosomes are concentratedin southern Europe (Cruciani et al. 2004), whereas thesmaller average divergence times between Europe and Africa relativeto East Asia and Africa are still readily apparent across each individualnorthern European sample population (Supplemental Table2). This suggests that the discrepancy has, at least partially, aneven earlier andmore pervasive origin, being established prior to theappearance, and consequent migration tagging ability, of the currentrange of mtDNA and Y-chromosome haplogroups."

"A second potential solution would interpret African-West Eurasian closeness not as evidence of a common population element in West Eurasians and Africans, but as a consequence of a population element in East Asians that both West Eurasians and Africans lack. The obvious candidate for such an element involves archaic admixture in East Asians. This is no longer an exotic possibility, given the evidence for such admixture that the sequencing of the Neandertal and Denisovan genome has produced".

I have long been sure that to be the case. The haplogroups are ex-Africa but that population mixed with others around the world. Makes the most sense to me. Otherwise we have a great deal of difficulty explainung the regional diversity of the modern human population.

There is probably a combination of factors, local admixture being one, but haplogroup ED certainly is intriguing.

In simple models you get this contradiction that D in East Asia appears old, while E in Africa makes it and perhaps Europe younger. I think a dual migration can resolve this if it at first succeeded to penetrate far east, but wasn't very successful. If much of the "green Sahara" and first ooA ~130,000 - 100,000 ya turned NE African CT to DE, there, this could have left D in East Asia and an E population in North Africa. A second migration 80,000-60,000 ya may have been more successful, bringing CT later-turned-CF from the Horn of Africa along the southern route outside. Where this mixed with a simultaneously spreading (via the Levant, or even or pre-existing) E population in West Asia, those retained some of their proximity to E and thus to what later dominated Africa (appearing "younger" even though, in a sense, being older). CF, expanding rapidly in SE Asia and later East Asia and the Americas, meanwhile is more removed from the now E-dominated Africa and thus appears more distant.

E then was isolated for ~60,000 years in North Africa, separated by the then-dry Sahara, accounting for it's small diversification despite its old age. Similarly, D was isolated in small pockets in East Asia for a similar time span. Any CT descendants in East Africa died out by the spreading E from the north, perhaps exactly being the force that drove them ooA in the second migration, in the first place. In addition, these people would also have been in contact with S and SE African populations for 60,000 years, removing them further from the extreme northern isolate.

So I guess this would applies to Eastern Eurasians relative to Native Americans. Although I would think we would not be able to tell without estimating the Native American effective populaton size to dismiss bottlenecks in that case?

In Oceania, archaic admixture could present the "push" factor pushing Oceanians away from West Eurasians and Africans relative to East Eurasians, but this would not apply in the Americas, unless we took the stance that there were unknown humans living in the Americas. So it seems implausible (based on present data) that encountering archaic populations in the Americas would push Native Americans further from Africans and Europeans than East Asians are, which is the case. So, in the absence of bottlenecks, more recent genetic dispersals involving East Eurasia subsequent to East Eurasian/American divergence seem required, either:

a) to and from Africa to East Eurasia or b) to East Eurasia via West Eurasians affected by African / who have affected Africans through gene flow or c) by from East Eurasia following divergence with Native Americans back to Europeans and Africans

In previous ADMIXTURE posts, it was shown that the least related population to Africans are Native Americans, even less than East Asians.

North Africans are akin to Europeans (and vice-versa). I don't know if this "African" component includes North Africans or not. If it does, then much of this can be easily explained.

If it's the archaic admixture in East Asians, this means the Native Americans have even more archaic admixture than any other group, which seems unlikely, but if that's the case, that'd contradict the idea that Europeans are descended from Asians who populated Europe in the last 7.000 years. The Melanesians have more admixture than East Asians, if that's correct they'd be the less related to Africans.

"In simple models you get this contradiction that D in East Asia appears old, while E in Africa makes it and perhaps Europe younger. I think a dual migration can resolve this"

We don't need to postulate a double migration if we're prepared to accept a mixture with East Asian archaics. Perhaps just one B Y-haps moved out of Africa and coalesced as CT. There it broke into two, CF and DE, spread through its geographic range. Members of DE moved both east and back into Africa. We know that several mtDNAs moved from SW Asia back into Africa so it's reasonable to assume some Y-hap did as well. In the far East Y-haps C and D and their associated autosomal DNA introgressed into the East Asian archaics.

"If it's the archaic admixture in East Asians, this means the Native Americans have even more archaic admixture than any other group, which seems unlikely"

It's possible under the above scenario. The population from Northeast Eurasia was able to enter America before a more 'African' population was able to reach the northeast.

"E then was isolated for ~60,000 years in North Africa, separated by the then-dry Sahara, accounting for it's small diversification despite its old age".

Maju would disagree with that. He claimed elsewhere that the expansion of E1b1b1 and E1b1a is Paleolithic. I agree that their 'age' may be Paleolithic but their 'expansion' can hardly be. And certainly their arrival in Europe can hardly be Paleolithic.

I just gave one of many examples of how several problems could be resolved in one. DE is a problem, as are many other unresolved issues. As deep-routed population structure in Africa has been proposed, and likely was present 300,000 to 130,000 ya - so also there may have been very important structure 130,000 to 60,000 ya, and we know the latter is extremely likely, given the 'Green Sahara" and the documented, continued modern population in North Africa, then.

E may appear more recent simply because it seems to originate from such pockets - but before neolithic expansions, it may have easily been isolated there a lifetime before, due to much more sever climate.

"I believe that the best signal of such a potential back-migration involves haplogroup E..its sister haplogroup D occurs as a relic in Asia, among people such as Tibetans, Ainu, or Andaman Islanders."

This would result in a greater similarity between Africans and Asians, not Africans and Europeans. E1b1 found only in southern Europe doesn't account for the same degree of proximity to Africans among all West Eurasians, as you pointed out.

"An early movement of DE-bearing men from Arabia into East Africa would serve to bring a West Eurasian autosomal component into Africa."

But hg D is not found in Arabia.

"consequence of a population element in East Asians that both West Eurasians and Africans lack.

The obvious candidate for such an element involves archaic admixture in East Asians. This is no longer an exotic possibility, given the evidence for such admixture that the sequencing of the Neandertal and Denisovan genome has produced."

The Denisovan component popped only in Papuans, not in East Asians. The Neanderthal admixture is shared equally between West and East Eurasians, at least from the meager data that we have. So, again, we don't have a good fit between data and theory.

What the paper misses entirely is the role of Amerindians in producing the current genetic variation in the Old World. The authors didn't even include Amerindians in the study because of the usual bizarre prejudice. A "population element" in East Asians missing in West Eurasians and Africans could be the Amerindian component. A relatively recent admixture from Amerindians into East Asians could push East Asians away from Africans and Europeans. The recently established linguistic link between Ket and Na-Dene can be an example of this admixture. On a broader scale, the generalized Mongoloid morphology first appears in the archaeological record in North America and only somewhat later in Asia. Y-DNA and mtDNA haplogroups common in Amerindians are often found at low frequencies in Northeast Asia. The Amerindian component can be very old, however, as in basally old, as the high frequency of "Neanderthal" B006 haplogroup on X chromosome attests.

@Oh-willeke

"It also has to explain trace presence of very basal versions of Y-DNA hg D in West Africa, apparently unrelated to any recent migrations from e.g. Tibet where basal hgs of Y-DNA hg D are found, while there is an absence of even trace levels of Y-DNA hg E in Asian locations that are rich in Y-DNA hg D (e.g. Andaman Islands, Siberia, Tibet, Japan)."

As usual, Andrew, you are being counterfactual. For more accurate information, see no. 14 here http://blogs.discovermagazine.com/gnxp/2011/03/the-day-of-the-farmer/

@neandertalerin

"If it's the archaic admixture in East Asians, this means the Native Americans have even more archaic admixture than any other group, which seems unlikely"

You've hit the problem right on the button. The so-called "archaic" admixture is often found at high frequencies in Amerindians (including blood group O detected in 2 Neandertals) but since there were no archaic hominids in the Americas, it's likely that it's the trace of common descent between humans and Eurasian hominids that survived in the isolated New World populations better than in Asian humans. Predictably, this component petered away geographically as populations moved out to Europe and Africa. This would solve the "problem" of greater proximity between Europeans and Africans, as these geographies are roughly equally removed from the source of human dispersal.

"The so-called "archaic" admixture is often found at high frequencies in Amerindians (including blood group O detected in 2 Neandertals)"

O blood group is archaic? It is also the most common blood group in Europe and most Africa. Many native American tribes (specially those from the north) have a very high incidence of A group. These blood groups likely evolved many thousands of years ago, even before the divergence of neandertals and modern humans, I guess. Maybe O blood was most common in neandertals (very few have been analyzed to date) but this doesn't necessarily mean they're related to Amerinds, or at least I don't see any reason to think it.

The transition from the Middle to the Upper Palaeolithic, approximately 40,000 years ago, marks a turning point in the history of human evolution in Europe. Many changes in the archaeological and fossil record at this time have been associated with the appearance of anatomically modern humans. It is generally believed that this vast region was not colonized by humans until the final stage of the last Ice Age some 13,000-14,000 years ago. But by 1998 we got the discovery of human occupation nearly 40,000 years old at Mamontovaya Kurya, a Palaeolithic site situated in the European part of the Russian Arctic. Since then we have had a number of sites within the arctic circle that show 'modern humans' more than 35 millenias old.

By the end of ice-age some of these palefaced, arctic peoples seem to have moved out of their refugia - and travelled south to become tanned and discover the indigenous peoples of the Eurasian continent.

That may have taken some of them to the northern tiers of America as well as to the snowy mountains of NW Africa.

"The implication that the far northern tier of Eurasia was occupied very early by modern humans is another piece of evidence consistent with the idea that the first modern Europeans came from the far north. This hypothesis proposes that the features that people spread into the Palearctic as a rather specialized adaptation, and may have exploited a niche available to highly mobile, long-limbed, and culturally sophisticated people."

I deliberately placed archaic in quotation marks. I don't think there's any "archaic admixture" in modern humans. What we see instead is continuity with some Eastern archaic populations best preserved in the New World and, apparently, Oceania. We don't have any genetic evidence for regional continuity in Africa, although it's a central prediction of the Oout of Africa model. Of course, we need more data on blood groups in neandertals but it's startling that they tested positive for blood group O. As humans colonized the Old World, and Africa, the frequencies of blood group O decreased everywhere but America and, possibly Australia where blood group O is also very frequent.

Not at all. There's plenty of evidence for "archaic admixture" in Amerindians. But since there were no archaic hominids in America, the following roster documents traces of continuity with Eastern hominids best preserved in the new World, and sometimes Oceania.

BTW, are you sure it's 0% Neandertal and 1% Denisovan? When I originally studied the data I remember seeing that they did not test Amerindians for Neandertal admixture and they found 0.9% of Denisovan admixture in Karitiana (next lowest after Africans).

"What we see instead is continuity with some Eastern archaic populations best preserved in the New World and, apparently, Oceania".

I can agree with that. I just couldn't see how you could maintain that modern humans had developed originally in America. Admixture with 'Eastern archaic populations' would explain much about your observations concerning kinship systems.

"I just couldn't see how you could maintain that modern humans had developed originally in America. Admixture with 'Eastern archaic populations' would explain much about your observations concerning kinship systems."

It's very easy, Terry. Speciation can only occur in isolation and the survival of a new species is facilitated by the geographic sparseness of competing species. The New World is the only major region that doesn't have big apes and didn't have homininds. (From this fact, people made a non-sequitur conclusion that humans must be recent in America.) But it's adjacent to the region with hominids (Neanderthals and Asian Homo erectus). This is a perfect set up for our species to emerge. The reason why Amerindians have traces of "archaic hominids" at higher frequencies than Old World humans is because a population of Eastern hominids went through a bottleneck, reduced its diversity, migrated across the Bering Strait into a new territory (America) speciated into "us" and then, with another retreat of the glacier, migrated back already as a new species capable of replacing their erstwhile hominid brethren in Asia, Europe and Africa. This is exactly what happened with woolly mammoths. http://www.cell.com/current-biology/abstract/S0960-9822%2808%2900970-6

As Homo sapiens sapiens fanned out, they expanded in size (on a number of consecutive occasions), which was required to colonize the huge Old World terrain. The frequency of the old "continuity alleles" went down as new mutations took over. Places like Sub-Saharan Africa became a magnet for several waves of expanding populations, hence it ended up having lots of diversity. The New World continues to preserve the archaic signature better than any other region because population size remained as low as it used to be in Middle Pleistocene when populations tended to drift apart without much intermixing.

Kinship systems cannot possibly be explained through admixture with Eastern hominids because Amerindian kinship systems (and to a lesser degree Australian and Oceanic) constitute not a weird insertion into standard human kinship structure but a logical basal point for their evolution, from small-scale isolated high inbreeding demography to large-scale intermixing low inbreeding demography.

There's been a lot of gene flow between North Africa, Europe and West Asia. There's an expansion from Nubia about 24k ago (the E1 Y chr)that ended up affecting the neolithic population of Europe and probably crossed over the SOG into the LGM population of Iberia. You also get West Asian Neolithic and Holocene ancestry shared between Africa and Europe, which could account for a lot of the closeness.

I'm placing the YAP mutation as happening on the Nile valley during the expansion out of Africa. The E Y chr mainly turned West back into North Africa (Jebel Irhoud)and the D (mainly) headed across the Sinia.

Can't think of a better place for a bottleneck than a long thin river valley winding through a desert.

"Can't think of a better place for a bottleneck than a long thin river valley winding through a desert".

And I think that is the reason why so few haplogroups made it out of Africa in the first place. To me the Bab al Mandab route along the Arabian coast has never been at all convincing. There is absolutley no evidence for it anyway.

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